Research workbench
Napa protein from borrelia burgdorferi
Analyse Napa protein from borrelia burgdorferi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PYB
- Type
- protein
- Length
- 604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil activating protein
- UniProt
- O51633
- Ligands
- FE
- Pockets
- 13 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 60% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neutrophil activating protein | protein | 151 | 60% helix, 0% strand | O51633 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.59 | 0.84 | 34 | empty |
| 2 | 204 | 0.56 | 0.79 | 21 | empty |
| 3 | 175 | 0.47 | 0.76 | 32 | FE |
| 4 | 73 | 0.45 | 0.81 | 18 | empty |
| 5 | 51 | 0.44 | 0.84 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1655 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1650 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 649 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 470 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2PYB · Napa protein from borrelia burgdorferi · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O51633
- Elsewhere: RCSB PDB 2PYB · PDBe 2PYB · UniProt O51633
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